Partitioning and distribution of RAPD variation in a forest tree species, Eucalyptus globulus (Myrtaceae)

Microsatellite analysis of population structure in Eucalyptus globulus

Eucalyptus globulus subsp. globulus Labill. (Tasmanian Blue Gum), native to southeast Australia, is a benchmark species for the pulp and paper industry. We genotyped 397 trees from 16 populations of E. globulus representing the native diversity in Australia using 24 microsatellite loci. Eight genetically distinct groups were detected, consistent with genetic groupings detected in previous quantitative and molecular studies. A sample of 29 Portuguese individuals was added to help clarify the origin of the Portuguese landrace. The results suggest a southern and eastern Tasmania origin for the Portuguese landrace. This genetic framework will enable researchers to investigate the provenance of individuals of unknown pedigree and assess the levels of representation of E. globulus natural variation in the Portuguese landrace.

Assessment of genetic diversity in indigenous turmeric (Curcuma longa) germplasm from India using molecular markers

Curcuma longa L., commonly known as turmeric, is one of the economically and medicinally important plant species. It is predominantly cultivated in the tropical and sub tropical countries. India is the largest producer, and exporter of turmeric in the world, followed by China, Indonesia, Bangladesh and Thailand. In the present study, Directed Amplification of Minisatellite DNA (DAMD) and Inter Simple Sequence Repeats (ISSR), methods were used to estimate the genetic variability in indigenous turmeric germplasm. Cumulative data analysis for DAMD (15) and ISSR (13) markers resulted into 478 fragments, out of which 392 fragments were polymorphic, revealing 82 % polymorphism across the turmeric genotypes. Wide range of pairwise genetic distances (0.03-0.59) across the genotypes revealed that these genotypes are genetically quite diverse. The UPGMA dendrogram generated using cumulative data showed significant relationships amongst the genotypes. All 29 genotypes studied grouped into two clusters irrespective of their geographical affiliations with 100 % bootstrap value except few genotypes, suggesting considerable diversity amongst the genotypes. These results suggested that the current collection of turmeric genotypes preserve the vast majority of natural variations. The results further demonstrate the efficiency and reliability of DAMD and ISSR markers in determining the genetic diversity and relationships among the indigenous turmeric germplasm. DAMD and ISSR profiling have identified diverse turmeric genotypes, which could be further utilized in various genetic improvement programmes including conventional as well as marker assisted breeding towards development of new and desirable turmeric genotypes.

Population genetic analysis and phylogeny reconstruction in Eucalyptus (Myrtaceae) using high-throughput, genome-wide genotyping

A set of over 8000 Diversity Arrays Technology (DArT) markers was tested for its utility in high-resolution population and phylogenetic studies across a range of Eucalyptus taxa. Small-scale population studies of Eucalyptus camaldulensis, Eucalyptus cladocalyx, Eucalyptus globulus, Eucalyptus grandis, Eucalyptus nitens, Eucalyptus pilularis and Eucalyptus urophylla demonstrated the potential of genome-wide genotyping with DArT markers to differentiate species, to identify interspecific hybrids and to resolve biogeographic disjunctions within species. The population genetic studies resolved geographically partitioned clusters in E. camaldulensis, E. cladocalyx, E. globulus and E. urophylla that were congruent with previous molecular studies. A phylogenetic study of 94 eucalypt species provided results that were largely congruent with traditional taxonomy and ITS-based phylogenies, but provided more resolution within major clades than had been obtained previously. Ascertainment bias (the bias introduced in a phylogeny from using markers developed in a small sample of the taxa that are being studied) was not detected. DArT offers an unprecedented level of resolution for population genetic, phylogenetic and evolutionary studies across the full range of Eucalyptus species.

Genetic diversity among Zygophyllum (Zygophyllaceae) populations based on RAPD analysis

Zygophyllum species are succulent plants that are drought resistant and/or salt tolerant, growing under severe, dry climatic conditions. Despite their importance and abundance in the Mediterranean and Middle East regions, there is little information concerning molecular variations among species of this genus. Genetic diversity was assessed, using RAPD primers, of 12 populations of Z. coccineum, Z. album and Z. aegyptium collected from various locations in Egypt and Saudi Arabia. Yong leaves were used for DNA extraction. Genetic distances were calculated using Nei's method. A dendrogram was constructed based on the similarity data matrix by unweighted pair group method using arithmetic averages cluster analysis. Analysis with RAPD markers revealed genetic variation between and within populations of Zygophyllum. Zygophyllum coccineum showed higher levels of genetic variation and more unique alleles than the other species.

AFLP analyses on genetic diversity and structure ofEupatorium adenophorumpopulations in China

Eupatorium adenophorum(crofton weed) is one of the most widespread invasive species in China. Its genetic diversity and population structure in China were analysed by amplified fragment length polymorphism (AFLP). Three primer pairs were selected for the analysis and 490 bands were produced from 62E. adenophorumpopulations selected from five major geographic areas. A total of 328 of the bands showed polymorphism [percentage of polymorphic bands (PPB)=59.4%]. Diversity levels of populations were relatively high (mean expected heterozygosity=0.154, mean Shannon index=0.241). At the regional level, the AMOVA indicated that about 70.25% of variation in the data set was from genotypic variations within populations, whereas 8.04% of the variation was due to regional differences, and the remaining 21.71% to differences among populations within the provincial regions. Cluster analysis based on the unweighted pair-group method using the method of arithmetic averages (UPGMA) grouped the majority ofE. adenophorumpopulations into four main clusters, which correspond to their geographic regions. It is concluded thatE. adenophorumspread mainly by wind or water and its genetic diversity level in newly invaded areas was lower than that in formerly colonized areas.

Eucalyptus applied genomics: from gene sequences to breeding tools

Eucalyptus is the most widely planted hardwood crop in the tropical and subtropical world because of its superior growth, broad adaptability and multipurpose wood properties. Plantation forestry of Eucalyptus supplies high-quality woody biomass for several industrial applications while reducing the pressure on tropical forests and associated biodiversity. This review links current eucalypt breeding practices with existing and emerging genomic tools. A brief discussion provides a background to modern eucalypt breeding together with some current applications of molecular markers in support of operational breeding. Quantitative trait locus (QTL) mapping and genetical genomics are reviewed and an in-depth perspective is provided on the power of association genetics to dissect quantitative variation in this highly diverse organism. Finally, some challenges and opportunities to integrate genomic information into directional selective breeding are discussed in light of the upcoming draft of the Eucalyptus grandis genome. Given the extraordinary genetic variation that exists in the genus Eucalyptus, the ingenuity of most breeders, and the powerful genomic tools that have become available, the prospects of applied genomics in Eucalyptus forest production are encouraging.

Parallel evolution of dwarf ecotypes in the forest tree Eucalyptus globulus

Three small populations of a dwarf ecotype of the forest tree Eucalyptus globulus are found on exposed granite headlands in south-eastern Australia. These populations are separated by at least 100 km. Here, we used 12 nuclear microsatellites and a chloroplast DNA marker to investigate the genetic affinities of the dwarf populations to one another and to their nearest populations of tall E. globulus. Cape Tourville was studied in greater detail to assess the processes enabling the maintenance of distinct ecotypes in close geographical proximity. The three dwarf populations were not related to one another and were more closely related to adjacent tall trees than to one another. At Cape Tourville the dwarf and tall ecotypes were significantly differentiated in microsatellites and in chloroplast DNA. The dwarf and tall populations differed in flowering time and no evidence of pollen dispersal from the more extensive tall to the dwarf population was found. The three dwarf populations have evolved in parallel from the local tall ecotypes. This study shows that small marginal populations of eucalypts are capable of developing reproductive isolation from nearby larger populations through differences in flowering time and/or minor spatial separation, making parapatric speciation possible.

Detection and visualization of spatial genetic structure in continuous Eucalyptus globulus forest

Visualizing the pattern of variation using microsatellites within a Eucalyptus globulus forest on the island of Tasmania provided surprising insights into the complex nature of the fine-scale spatial genetic structure that resides in these forests. We used spatial autocorrelation and principal coordinate analysis to compare fine-scale genetic structure between juvenile and mature cohorts in a study area, 140 m in diameter, located within a typical, continuous E. globulus forest. In total, 115 juvenile and 168 mature individuals were genotyped with eight highly polymorphic microsatellite loci. There was no significant difference in the level of genetic diversity between cohorts. However, there were differences in the spatial distribution of the genetic variation. Autocorrelation analysis provided clear evidence for significant spatial genetic structure in the mature cohort and significant, but weaker, structure in the juvenile cohort. The spatial interpolation of principal coordinate axes, derived from ordination of the genetic distance matrix between individuals, revealed a spatially coherent family group which was evident in both cohorts. Direct comparison of the genetic structure within each cohort allowed visualization of a shift in the spatial distribution of genetic variation within the population of approximately 10 m. As the shift coincided with the direction of prevailing winds, it is hypothesized that this phenomenon is due to downwind dispersal of seeds and is indicative of the important role of prevailing winds in forcing eastward gene flow in these high-latitude forests.

Quantitative trait loci analysis for the developmental behavior of Soybean (Glycine max L. Merr.)

Quantitative trait loci (QTLs) identified so far in soybean were mainly derived in the final stage of plant development, which did not apply to the exploitation of genetic effects that were expressed during a specific developmental stage. Thus, the aim of this study was to identify conditional QTLs associated with yield traits at a specific developmental interval of soybean plant. The 143 recombinant inbred lines developed from the cross of soybean cultivars 'Charleston' and 'Dongnong 594' were used for the developmental QTLs analysis of pod number in the main stem and plant height by composite interval mapping method combined with mixed genetic model. The results indicated that the number and type of QTLs and their genetic effects for the two agronomic traits were different in a series of measuring stages. A total of 10 unconditional QTLs in 6 linkage groups and 5 conditional QTLs in 3 linkage groups were identified for the pod number of the main stem, while 13 unconditional QTLs in 7 linkage groups and 12 conditional QTLs in 6 linkage groups were identified for plant height. Many QTLs that were detected in the early stages were different from those detected at the later stages. Some QTLs existed only at one stage and others existed across two or three stages. Five marker intervals (satt509-satt251, sat_099-sat_113, sat_113-OPAW19_4, satt457-OPC10_85, sat_095-OPBA08_5) were proven to be associated both with the development of pod number in the main stem and the development of plant height. The present study suggested that the development of pods and plant height in soybean were governed by time-dependent gene expression.

Power of microsatellite markers for fingerprinting and parentage analysis in Eucalyptus grandis breeding populations

We report the genetic analysis of 192 unrelated individuals of an elite breeding population of Eucalyptus grandis (Hill ex Maiden) with a selected set of six highly polymorphic microsatellite markers developed for species of the genus Eucalyptus. A full characterization of this set of six loci was carried out generating allele frequency distributions that were used to estimate parameters of genetic information content of these loci, including expected heterozygosity, polymorphism information content (PIC), power of exclusion, and probability of identity. The number of detected alleles per locus ranged from 6 to 33, with an average of 19.8 +/- 9.2. The average expected heterozygosity was 0.86 +/- 0.11 and the average PIC was 0.83 +/- 0.16. Using only three loci, it was possible to discriminate all 192 individuals. The overall probability of identity considering all six EMBRA microsatellite markers combined was lower than 1 in 2 billion. An analysis of the sample size necessary to estimate expected heterozygosity with minimum variance indicated that at least 64 individuals have to be genotyped to characterize this parameter with adequate accuracy for most microsatellites in Eucalyptus. The high degree of multiallelism and the clear and simple codominant Mendelian inheritance of the set of microsatellites used provide an extremely powerful system for the unique identification of Eucalyptus individuals for fingerprinting purposes and parentage testing.

Glacial refugia and reticulate evolution: the case of the Tasmanian eucalypts

Tasmania is a natural laboratory for investigating the evolutionary processes of the Quaternary. It is a large island lying 40-44 degrees S, which was repeatedly glaciated and linked to southeastern continental Australia during the Quaternary. Climate change promoted both the isolation of species in glacial refugia, and an exchange between Tasmanian and mainland floras. Eucalyptus is a complex and diverse genus, which has increased in abundance in Australia over the past 100 kyr, probably in response to higher fire frequency. Morphological evidence suggests that gene flow may have occurred between many eucalypt species after changes in their distribution during the Quaternary. This paper summarizes recent genetic evidence for migration and introgressive hybridization in Tasmanian Eucalyptus. Maternally inherited chloroplast DNA reveals a long-term persistence of eucalypts in southeastern Tasmanian refugia, coupled with introgressive hybridization involving many species. Detailed analysis of the widespread species Eucalyptus globulus suggests that migration from mainland Australia was followed by introgression involving a rare Tasmanian endemic. The data support the hypothesis that changes in distribution of interfertile species during the Quaternary have promoted reticulate evolution in Eucalyptus.

Inheritance of plant regeneration from maize (Zea mays L.) shoot meristem cultures derived from germinated seeds and the identification of associated RAPD and SSR markers

The inheritance of shoot regeneration through shoot-tip meristem culture derived from maize seedling was evaluated, and the markers (RAPD and SSR) associated with this regeneration character were identified both in a group of North American maize inbreds and a crossing population. A discrete distribution of percent regeneration and no. of shoots per explant was observed in the inbred group and the F(2) population. The results suggested that this regenerable trait was controlled by several major genes. Five RAPD markers were identified to be relevant to percent regeneration in maize shoot-tip culture system. One RAPD marker and three SSR markers were associated with no. of shoot per explant and its relevant traits. Of them marker BC603-1600 explained 18% of the variation for no. of shoot per explant and 16% of the variation for callus size. The BC603-1600 was sequenced and assigned in linkage group 7 based on a NCBI blast search. The information provided here should benefit to determine the genetic mechanisms involved in the maize regeneration response related to shoot meristem culture pathway and benefit to select high regenerable germplasm by using marker assisted selection.

Morphological and molecular data to determine the origin and taxonomic status of Prosopis chilensis var. riojana (Fabaceae, Mimosoideae)

This study analyzes the morphological and genetic characteristics of three sympatric populations of Prosopis from Argentina. Although morphological and geographical data suggest that Prosopis chilensis var. riojana is an interspecific hybrid of Prosopis chilensis var. chilensis and Prosopis flexuosa var. flexuosa, no correlation was found between morphological traits and genetic distances generated by random amplified polymorphic DNA - polymerase chain reaction (RAPD-PCR). Genetic similarity is greater among P. chilensis var. chilensis and P. flexuosa var. flexuosa than between either of these two taxa with P. chilensis var. riojana. Also, P. chilensis var. riojana has unique genetic markers that are absent from its putative parents. Additionally, dendrograms generated by unweighted pair group method with arithmetic means (UPGMA) and Neighbor-Joining clustering criteria group P. chilensis var. chilensis and P. flexuosa var. flexuosa apart from P. chilensis var. riojana. Possibilities for the lack of congruence between morphology and RAPD markers are discussed. The results obtained are insufficient to conclusively establish the origin of P. chilensis var. riojana; however, the morphological and genetic traits observed suggest this taxon is well differentiated from P. chilensis var. chilensis and P. flexuosa var. flexuosa.Key words: genetic distances, hybridization, morphology, Prosopis, RAPD, rare taxon.

Analysis of genetic diversity and structure in Ethiopian populations of Phytolacca dodecandra using RAPD

The genetic diversity and structure in 17 wild populations (249 individuals) of Phytolacca dodecandra (endod) sampled along altitudinal gradients of 1600-3000 meters above sea level (m.a.s.l.) in Ethiopia was studied using random amplified polymorphic DNA (RAPD). A total of 70 polymorphic loci (P) scored from 12 RAPD primers were used to calculate different diversity indices within and between populations, habitats, geographical regions, climatic zones and altitude groups. The number of polymorphic loci and overall Shannon information measure (H) in the populations varied from 30 to 55 and from 0.228 to 0.418, respectively. In general, differences in population variability were found significantly correlated to effective population size. Both P and H were significantly higher in an undisturbed than in a disturbed habitat, and in the lowland and central-highland than in the highland altitude group. However, for both parameters the differences were not statistically significant between regions and climatic zones. Genetic distance between populations varied from 0.301 to 0.628. Cluster analysis performed using the genetic distance matrix revealed a clear separation of the highland populations (2501-3000 m.a.s.l.) from those of the lowland/central-highlands (1600-2500 m.a.s.l.) irrespective of their geographical regions and climatic zones. Analysis of molecular variance (AMOVA) indicated that differences in habitat, geographical regions and climatic zones explained 4.6%, 2.5% and 4.6%, respectively. But none of these differences were significant. Altitude explained 17.2% of the total variance and was highly significant. The data, therefore, clearly indicated the association of genetic structure in endod with altitude. The proportion of RAPD variation found among populations (21.2-35.0%) was somewhat intermediate between values reported for selfing and outcrossing species. The fixation index (FST) values (0.350 to 0.384) indicated very high genetic differentiation among populations.

Genetic differentiation of Euterpe edulis Mart. populations estimated by AFLP analysis

Heart-of-palm (Euterpe edulis Mart.) is a wild palm with a wide distribution throughout the Atlantic Rainforest. Populations of E. edulis represent important renewable natural resources but are currently under threat from predatory exploitation. Furthermore, because the species is indigenous to the Atlantic Rainforest, which is located in the most economically developed and populated region of Brazil, social and economic pressures have devastated heart-of-palm forests. In order to estimate the partitioning of genetic variation of endangered E. edulis populations, 429 AFLP markers were used to analyse 150 plants representing 11 populations of the species distribution range. Analysis of the genetic structure of populations carried out using analysis of molecular variance (AMOVA) revealed moderate genetic variation within populations (57. 4%). Genetic differentiation between populations (FST = 0.426) was positively correlated with geographical distance. These results could be explained by the historical fragmentation of the Atlantic coastal region, together with the life cycle and mating system. The data obtained in this work should have important implications for conservation and future breeding programmes of E. edulis.

Conservation genetics of bush mango from central/west Africa: implications from random amplified polymorphic DNA analysis

Genetic variation was assessed in the two bush mango species, Irvingia gabonensis and I. wombolu, valuable multipurpose fruit trees from central and west Africa that are currently undergoing domestication. A total of 130 individuals sampled from Cameroon, Nigeria and Gabon were analysed using 74 random amplified polymorphic DNAs (RAPDs). Significant genetic integrity was found in the two morphologically similar species (among-species analysis of molecular variance [AMOVA] variance component 25.8%, P < 0.001), with no evidence of hybridization, even between individuals from areas of sympatry where hybridization was considered probable. Results suggest that large-scale transplantation of either species into new habitats will probably not lead to genetic introgression from or into the other species. Therefore, subsequent cultivation of the two species should not be hindered by this consideration, although further studies on the potential for hybridization/introgression between these species would be prudent. Significant genetic differentiation of both species (among-countries within species, nested AMOVA variance component 9.8%, P < 0.001) was observed over the sampled regions, and genetic similarity of samples decreased significantly with increasing geographical distance, according to number of alleles in common (NAC) analysis. 'Hot spots' of genetic diversity were found clustered in southern Nigeria and southern Cameroon for I. wombolu, and in southern Nigeria, southern Cameroon and central Gabon for I. gabonensis. The possible reasons for this distribution of genetic variation are discussed, but it may reflect evolutionary history, as these populations occur in areas of postulated Pleistocene refugia. The application of these results to domestication programmes and, in the light of extensive deforestation in the region, conservation approaches, is discussed.

Random amplified polymorphic DNA analysis of southern brown bandicoot (Isoodon obesulus) populations in Western Australia reveals genetic differentiation related to environmental variables

Random amplified polymorphic DNA (RAPD) markers were used to analyse genetic variation within and between populations of Isoodon obesulus in Western Australia. Genetically controlled geographical variation in body size associated with habitat type and rainfall exists in this species, raising the question of whether local conditions may influence gene flow in I. obesulus. The RAPD markers displayed substantial genetic variation, with all animals possessing unique RAPD phenotypes over 39 polymorphic bands produced by three primers. Significant geographical subdivision was apparent (PhiST = 0.208) with southwest locations being divergent from all others, despite there being no physical barriers to gene flow. The pattern of subdivision was unrelated to physical distance between the locations, but was related to both annual rainfall and habitat type. Therefore, the most reasonable explanation for this pattern of subdivision appears to be that gene flow is restricted by selection against migrants between local populations with substantially different habitat type or rainfall. Restriction of gene flow through selection against migrants is rarely investigated, and the results of this study suggest that the importance of this process in the formation of population structure may be underestimated.

Genetic diversity in mesoamerican populations of mahogany (Swietenia macrophylla), assessed using RAPDs

Swietenia macrophylla King, a timber species native to tropical America, is threatened by selective logging and deforestation. To quantify genetic diversity within the species and monitor the impact of selective logging, populations were sampled across Mesoamerica, from Mexico to Panama, and analysed for RAPD DNA variation. Ten decamer primers generated 102 polymorphic RAPD bands and pairwise distances were calculated between populations according to Nei, then used to construct a radial neighbour-joining dendrogram and examine intra- and interpopulation variance coefficients, by analysis of molecular variation (AMOVA). Populations from Mexico clustered closely together in the dendrogram and were distinct from the rest of the populations. Those from Belize also clustered closely together. Populations from Panama, Guatemala, Costa Rica, Nicaragua and Honduras, however, did not cluster closely by country but were more widely scattered throughout the dendrogram. This result was also reflected by an autocorrelation analysis of genetic and geographical distance. Genetic diversity estimates indicated that 80% of detected variation was maintained within populations and regression analysis demonstrated that logging significantly decreased population diversity (P = 0.034). This study represents one of the most wide-ranging surveys of molecular variation within a tropical tree species to date. It offers practical information for the future conservation of mahogany and highlights some factors that may have influenced the partitioning of genetic diversity in this species across Mesoamerica.

DNA profiling resolves the limited importance of flower colour in defining varieties of Lantana camara

Randomly amplified polymorphic DNA (RAPD), successfully used to establish flower colour, is of limited importance in characterising weedy varieties of Lantana camara. Initially the internal transcribed spacer 1 (ITS1) region was sequenced for common pink and common pink-edged red varieties of L. camara from Australia and L. urticofolia from the neotropics. This proved unhelpful in differentiating varieties due to a lack of variation and the hybrid origin of L. camara, necessitating the utilisation of DNA profiling techniques. Unweighted pair group method arithmetic average (UPGMA) analysis of RAPD data demonstrated that geographical proximity contributes more significantly to genetic relatedness than flower colour. Analysis of molecular variance (AMOVA) likewise demonstrated that geography accounts for a relatively large variance component. These data indicate that the use of flower colour as a primary identification tool needs to be reevaluated. The use of RAPD may prove useful in characterising the weedy varieties of lantana present in Australia and the South Pacific. Since biological control efforts are being hindered by the inadequacy of current morphological taxonomy, it is expected that DNA profiling will underpin continuing studies on the management and control of L. camara.

Forest tree biotechnology

The forest products industry has traditionally viewed trees as merely a raw, and more or less immutable, natural resource. However, unlike such inanimate resources as metallic ores, trees have the potential to be modified genetically, essentially transmuting lead into gold. Increasingly, modern alchemists are applying the tools of biotechnology in efforts to reduce the biological constraints on forest productivity. Several new methodologies being used to address problems in forest biology are described with respect to their potential impact on forest tree improvement. In addition to addressing problems inherent to the current use of trees for production of pulp and paper or solid wood products, genetic manipulation of trees brings with it the potential to create new industries based on the novel characteristics of transgenic trees, e.g. trees containing transgenes to detoxify specific pollutants could be used in the remediation of sites contaminated with hazardous wastes. Efforts to modify trees through biotechnology are in their infancy, and this review seeks to outline the underpinnings of what will undoubtedly be an area of increased emphasis in the next millennium.

Population genetics of cultivated common buckwheat, Fagopyrum esculentum Moench. X. Diffusion routes revealed by RAPD markers

Diffusion routes of common buckwheat were investigated by constructing phylogenetic trees based on variability of RAPD markers among 46 land races and two natural populations of the ancestor. Thirty two primers out of 40 generated reliable RAPD bands, 295 in total. The percentage of polymorphic bands was the highest (45.9%) in southern China, the region in which buckwheat originated, and it declined sharply from southern China to the peripheral range of buckwheat cultivation. Phylogenetic trees for land races were constructed from RAPD variability by the unweighted pair group (UPG) and neighbors joining (NJ) methods. They suggest two major routes of diffusion of buckwheat cultivation; one from southern China-->northern China-->Korea-->Japan, the other from southern China-->Bhutan-->Nepal-->Kashmir-->Karakoram and the Hindukush.